@loaders.gl/geotiff 3.1.0-alpha.4 → 3.1.0-beta.3

package/dist/es5/lib/ome/ome-indexers.js.map

@@ -1 +1 @@
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However, modern version of Bioformats have a different\n * memory layout for pyramidal resolutions. Thus, we have two different \"indexers\"\n * depending on which format version is detected.\n *\n * TODO: We currently only support indexing the first image in the OME-TIFF with\n * our indexers. There can be multiple images in an OME-TIFF, so supporting these\n * images will require extending these indexers or creating new methods.\n */\n\n/*\n * Returns an indexer for legacy Bioformats images. This assumes that\n * downsampled resolutions are stored sequentially in the OME-TIFF.\n */\nexport function getOmeLegacyIndexer(tiff: GeoTIFF, rootMeta: OMEXML): OmeTiffIndexer {\n  const imgMeta = rootMeta[0];\n  const {SizeT, SizeC, SizeZ} = imgMeta.Pixels;\n  const ifdIndexer = getOmeIFDIndexer(imgMeta);\n\n  return (sel: OmeTiffSelection, pyramidLevel: number) => {\n    // Get IFD index at base pyramid level\n    const index = ifdIndexer(sel);\n    // Get index of first image at pyramidal level\n    const pyramidIndex = pyramidLevel * SizeZ * SizeT * SizeC;\n    // Return image at IFD index for pyramidal level\n    return tiff.getImage(index + pyramidIndex);\n  };\n}\n\n/*\n * Returns an indexer for modern Bioforamts images that store multiscale\n * resolutions using SubIFDs.\n *\n * The ifdIndexer returns the 'index' to the base resolution for a\n * particular 'selection'. The SubIFDs to the downsampled resolutions\n * of the 'selection' are stored within the `baseImage.fileDirectory`.\n * We use the SubIFDs to get the IFD for the corresponding sub-resolution.\n *\n * NOTE: This function create a custom IFD cache rather than mutating\n * `GeoTIFF.ifdRequests` with a random offset. The IFDs are cached in\n * an ES6 Map that maps a string key that identifies the selection uniquely\n * to the corresponding IFD.\n */\nexport function getOmeSubIFDIndexer(tiff: GeoTIFF, rootMeta: OMEXML): OmeTiffIndexer {\n  const imgMeta = rootMeta[0];\n  const ifdIndexer = getOmeIFDIndexer(imgMeta);\n  const ifdCache: Map<string, Promise<ImageFileDirectory>> = new Map();\n\n  return async (sel: OmeTiffSelection, pyramidLevel: number) => {\n    const index = ifdIndexer(sel);\n    const baseImage = await tiff.getImage(index);\n\n    // It's the highest resolution, no need to look up SubIFDs.\n    if (pyramidLevel === 0) {\n      return baseImage;\n    }\n\n    const {SubIFDs} = baseImage.fileDirectory;\n    if (!SubIFDs) {\n      throw Error('Indexing Error: OME-TIFF is missing SubIFDs.');\n    }\n\n    // Get IFD for the selection at the pyramidal level\n    const key = `${sel.t}-${sel.c}-${sel.z}-${pyramidLevel}`;\n    if (!ifdCache.has(key)) {\n      // Only create a new request if we don't have the key.\n      const subIfdOffset = SubIFDs[pyramidLevel - 1];\n      ifdCache.set(key, tiff.parseFileDirectoryAt(subIfdOffset));\n    }\n    const ifd = (await ifdCache.get(key)) as ImageFileDirectory;\n\n    // Create a new image object manually from IFD\n    // https://github.com/geotiffjs/geotiff.js/blob/8ef472f41b51d18074aece2300b6a8ad91a21ae1/src/geotiff.js#L447-L453\n    return new (baseImage.constructor as any)(\n      ifd.fileDirectory,\n      ifd.geoKeyDirectory,\n      tiff.dataView,\n      tiff.littleEndian,\n      tiff.cache,\n      tiff.source\n    ) as GeoTIFFImage;\n  };\n}\n\n/*\n * Returns a function that computes the image index based on the dimension\n * order and dimension sizes.\n */\nfunction getOmeIFDIndexer(imgMeta: OMEXML[0]): (sel: OmeTiffSelection) => number {\n  const {SizeC, SizeZ, SizeT, DimensionOrder} = imgMeta.Pixels;\n  switch (DimensionOrder) {\n    case 'XYZCT': {\n      return ({t, c, z}) => t * SizeZ * SizeC + c * SizeZ + z;\n    }\n    case 'XYZTC': {\n      return ({t, c, z}) => c * SizeZ * SizeT + t * SizeZ + z;\n    }\n    case 'XYCTZ': {\n      return ({t, c, z}) => z * SizeC * SizeT + t * SizeC + c;\n    }\n    case 'XYCZT': {\n      return ({t, c, z}) => t * SizeC * SizeZ + z * SizeC + c;\n    }\n    case 'XYTCZ': {\n      return ({t, c, z}) => z * SizeT * SizeC + c * SizeT + t;\n    }\n    case 'XYTZC': {\n      return ({t, c, z}) => c * SizeT * SizeZ + z * SizeT + t;\n    }\n    default: {\n      throw new Error(`Invalid OME-XML DimensionOrder, got ${DimensionOrder}.`);\n    }\n  }\n}\n"],"file":"ome-indexers.js"}
+{"version":3,"sources":["../../../../src/lib/ome/ome-indexers.ts"],"names":["getOmeLegacyIndexer","tiff","rootMeta","imgMeta","SizeT","SizeC","SizeZ","Pixels","ifdIndexer","getOmeIFDIndexer","sel","pyramidLevel","index","pyramidIndex","getImage","getOmeSubIFDIndexer","ifdCache","Map","baseImage","SubIFDs","fileDirectory","Error","key","t","c","z","has","subIfdOffset","set","parseFileDirectoryAt","ifd","get","constructor","geoKeyDirectory","dataView","littleEndian","cache","source","DimensionOrder"],"mappings":";;;;;;;;AAyBO,SAASA,mBAAT,CAA6BC,IAA7B,EAA4CC,QAA5C,EAA8E;AACnF,QAAMC,OAAO,GAAGD,QAAQ,CAAC,CAAD,CAAxB;AACA,QAAM;AAACE,IAAAA,KAAD;AAAQC,IAAAA,KAAR;AAAeC,IAAAA;AAAf,MAAwBH,OAAO,CAACI,MAAtC;AACA,QAAMC,UAAU,GAAGC,gBAAgB,CAACN,OAAD,CAAnC;AAEA,SAAO,CAACO,GAAD,EAAwBC,YAAxB,KAAiD;AAEtD,UAAMC,KAAK,GAAGJ,UAAU,CAACE,GAAD,CAAxB;AAEA,UAAMG,YAAY,GAAGF,YAAY,GAAGL,KAAf,GAAuBF,KAAvB,GAA+BC,KAApD;AAEA,WAAOJ,IAAI,CAACa,QAAL,CAAcF,KAAK,GAAGC,YAAtB,CAAP;AACD,GAPD;AAQD;;AAgBM,SAASE,mBAAT,CAA6Bd,IAA7B,EAA4CC,QAA5C,EAA8E;AACnF,QAAMC,OAAO,GAAGD,QAAQ,CAAC,CAAD,CAAxB;AACA,QAAMM,UAAU,GAAGC,gBAAgB,CAACN,OAAD,CAAnC;AACA,QAAMa,QAAkD,GAAG,IAAIC,GAAJ,EAA3D;AAEA,SAAO,OAAOP,GAAP,EAA8BC,YAA9B,KAAuD;AAC5D,UAAMC,KAAK,GAAGJ,UAAU,CAACE,GAAD,CAAxB;AACA,UAAMQ,SAAS,GAAG,MAAMjB,IAAI,CAACa,QAAL,CAAcF,KAAd,CAAxB;;AAGA,QAAID,YAAY,KAAK,CAArB,EAAwB;AACtB,aAAOO,SAAP;AACD;;AAED,UAAM;AAACC,MAAAA;AAAD,QAAYD,SAAS,CAACE,aAA5B;;AACA,QAAI,CAACD,OAAL,EAAc;AACZ,YAAME,KAAK,CAAC,8CAAD,CAAX;AACD;;AAGD,UAAMC,GAAG,aAAMZ,GAAG,CAACa,CAAV,cAAeb,GAAG,CAACc,CAAnB,cAAwBd,GAAG,CAACe,CAA5B,cAAiCd,YAAjC,CAAT;;AACA,QAAI,CAACK,QAAQ,CAACU,GAAT,CAAaJ,GAAb,CAAL,EAAwB;AAEtB,YAAMK,YAAY,GAAGR,OAAO,CAACR,YAAY,GAAG,CAAhB,CAA5B;AACAK,MAAAA,QAAQ,CAACY,GAAT,CAAaN,GAAb,EAAkBrB,IAAI,CAAC4B,oBAAL,CAA0BF,YAA1B,CAAlB;AACD;;AACD,UAAMG,GAAG,GAAI,MAAMd,QAAQ,CAACe,GAAT,CAAaT,GAAb,CAAnB;AAIA,WAAO,IAAKJ,SAAS,CAACc,WAAf,CACLF,GAAG,CAACV,aADC,EAELU,GAAG,CAACG,eAFC,EAGLhC,IAAI,CAACiC,QAHA,EAILjC,IAAI,CAACkC,YAJA,EAKLlC,IAAI,CAACmC,KALA,EAMLnC,IAAI,CAACoC,MANA,CAAP;AAQD,GAjCD;AAkCD;;AAMD,SAAS5B,gBAAT,CAA0BN,OAA1B,EAAiF;AAC/E,QAAM;AAACE,IAAAA,KAAD;AAAQC,IAAAA,KAAR;AAAeF,IAAAA,KAAf;AAAsBkC,IAAAA;AAAtB,MAAwCnC,OAAO,CAACI,MAAtD;;AACA,UAAQ+B,cAAR;AACE,SAAK,OAAL;AAAc;AACZ,eAAO,CAAC;AAACf,UAAAA,CAAD;AAAIC,UAAAA,CAAJ;AAAOC,UAAAA;AAAP,SAAD,KAAeF,CAAC,GAAGjB,KAAJ,GAAYD,KAAZ,GAAoBmB,CAAC,GAAGlB,KAAxB,GAAgCmB,CAAtD;AACD;;AACD,SAAK,OAAL;AAAc;AACZ,eAAO,CAAC;AAACF,UAAAA,CAAD;AAAIC,UAAAA,CAAJ;AAAOC,UAAAA;AAAP,SAAD,KAAeD,CAAC,GAAGlB,KAAJ,GAAYF,KAAZ,GAAoBmB,CAAC,GAAGjB,KAAxB,GAAgCmB,CAAtD;AACD;;AACD,SAAK,OAAL;AAAc;AACZ,eAAO,CAAC;AAACF,UAAAA,CAAD;AAAIC,UAAAA,CAAJ;AAAOC,UAAAA;AAAP,SAAD,KAAeA,CAAC,GAAGpB,KAAJ,GAAYD,KAAZ,GAAoBmB,CAAC,GAAGlB,KAAxB,GAAgCmB,CAAtD;AACD;;AACD,SAAK,OAAL;AAAc;AACZ,eAAO,CAAC;AAACD,UAAAA,CAAD;AAAIC,UAAAA,CAAJ;AAAOC,UAAAA;AAAP,SAAD,KAAeF,CAAC,GAAGlB,KAAJ,GAAYC,KAAZ,GAAoBmB,CAAC,GAAGpB,KAAxB,GAAgCmB,CAAtD;AACD;;AACD,SAAK,OAAL;AAAc;AACZ,eAAO,CAAC;AAACD,UAAAA,CAAD;AAAIC,UAAAA,CAAJ;AAAOC,UAAAA;AAAP,SAAD,KAAeA,CAAC,GAAGrB,KAAJ,GAAYC,KAAZ,GAAoBmB,CAAC,GAAGpB,KAAxB,GAAgCmB,CAAtD;AACD;;AACD,SAAK,OAAL;AAAc;AACZ,eAAO,CAAC;AAACA,UAAAA,CAAD;AAAIC,UAAAA,CAAJ;AAAOC,UAAAA;AAAP,SAAD,KAAeD,CAAC,GAAGpB,KAAJ,GAAYE,KAAZ,GAAoBmB,CAAC,GAAGrB,KAAxB,GAAgCmB,CAAtD;AACD;;AACD;AAAS;AACP,cAAM,IAAIF,KAAJ,+CAAiDiB,cAAjD,OAAN;AACD;AArBH;AAuBD","sourcesContent":["import type {GeoTIFFImage, GeoTIFF, ImageFileDirectory} from 'geotiff';\nimport type {OMEXML} from '../ome/omexml';\n\nexport type OmeTiffSelection = {t: number; c: number; z: number};\nexport type OmeTiffIndexer = (sel: OmeTiffSelection, z: number) => Promise<GeoTIFFImage>;\n\n/*\n * An \"indexer\" for a GeoTIFF-based source is a function that takes a\n * \"selection\" (e.g. { z, t, c }) and returns a Promise for the GeoTIFFImage\n * object corresponding to that selection.\n *\n * For OME-TIFF images, the \"selection\" object is the same regardless of\n * the format version. However, modern version of Bioformats have a different\n * memory layout for pyramidal resolutions. Thus, we have two different \"indexers\"\n * depending on which format version is detected.\n *\n * TODO: We currently only support indexing the first image in the OME-TIFF with\n * our indexers. There can be multiple images in an OME-TIFF, so supporting these\n * images will require extending these indexers or creating new methods.\n */\n\n/*\n * Returns an indexer for legacy Bioformats images. This assumes that\n * downsampled resolutions are stored sequentially in the OME-TIFF.\n */\nexport function getOmeLegacyIndexer(tiff: GeoTIFF, rootMeta: OMEXML): OmeTiffIndexer {\n  const imgMeta = rootMeta[0];\n  const {SizeT, SizeC, SizeZ} = imgMeta.Pixels;\n  const ifdIndexer = getOmeIFDIndexer(imgMeta);\n\n  return (sel: OmeTiffSelection, pyramidLevel: number) => {\n    // Get IFD index at base pyramid level\n    const index = ifdIndexer(sel);\n    // Get index of first image at pyramidal level\n    const pyramidIndex = pyramidLevel * SizeZ * SizeT * SizeC;\n    // Return image at IFD index for pyramidal level\n    return tiff.getImage(index + pyramidIndex);\n  };\n}\n\n/*\n * Returns an indexer for modern Bioforamts images that store multiscale\n * resolutions using SubIFDs.\n *\n * The ifdIndexer returns the 'index' to the base resolution for a\n * particular 'selection'. The SubIFDs to the downsampled resolutions\n * of the 'selection' are stored within the `baseImage.fileDirectory`.\n * We use the SubIFDs to get the IFD for the corresponding sub-resolution.\n *\n * NOTE: This function create a custom IFD cache rather than mutating\n * `GeoTIFF.ifdRequests` with a random offset. The IFDs are cached in\n * an ES6 Map that maps a string key that identifies the selection uniquely\n * to the corresponding IFD.\n */\nexport function getOmeSubIFDIndexer(tiff: GeoTIFF, rootMeta: OMEXML): OmeTiffIndexer {\n  const imgMeta = rootMeta[0];\n  const ifdIndexer = getOmeIFDIndexer(imgMeta);\n  const ifdCache: Map<string, Promise<ImageFileDirectory>> = new Map();\n\n  return async (sel: OmeTiffSelection, pyramidLevel: number) => {\n    const index = ifdIndexer(sel);\n    const baseImage = await tiff.getImage(index);\n\n    // It's the highest resolution, no need to look up SubIFDs.\n    if (pyramidLevel === 0) {\n      return baseImage;\n    }\n\n    const {SubIFDs} = baseImage.fileDirectory;\n    if (!SubIFDs) {\n      throw Error('Indexing Error: OME-TIFF is missing SubIFDs.');\n    }\n\n    // Get IFD for the selection at the pyramidal level\n    const key = `${sel.t}-${sel.c}-${sel.z}-${pyramidLevel}`;\n    if (!ifdCache.has(key)) {\n      // Only create a new request if we don't have the key.\n      const subIfdOffset = SubIFDs[pyramidLevel - 1];\n      ifdCache.set(key, tiff.parseFileDirectoryAt(subIfdOffset));\n    }\n    const ifd = (await ifdCache.get(key)) as ImageFileDirectory;\n\n    // Create a new image object manually from IFD\n    // https://github.com/geotiffjs/geotiff.js/blob/8ef472f41b51d18074aece2300b6a8ad91a21ae1/src/geotiff.js#L447-L453\n    return new (baseImage.constructor as any)(\n      ifd.fileDirectory,\n      ifd.geoKeyDirectory,\n      tiff.dataView,\n      tiff.littleEndian,\n      tiff.cache,\n      tiff.source\n    ) as GeoTIFFImage;\n  };\n}\n\n/*\n * Returns a function that computes the image index based on the dimension\n * order and dimension sizes.\n */\nfunction getOmeIFDIndexer(imgMeta: OMEXML[0]): (sel: OmeTiffSelection) => number {\n  const {SizeC, SizeZ, SizeT, DimensionOrder} = imgMeta.Pixels;\n  switch (DimensionOrder) {\n    case 'XYZCT': {\n      return ({t, c, z}) => t * SizeZ * SizeC + c * SizeZ + z;\n    }\n    case 'XYZTC': {\n      return ({t, c, z}) => c * SizeZ * SizeT + t * SizeZ + z;\n    }\n    case 'XYCTZ': {\n      return ({t, c, z}) => z * SizeC * SizeT + t * SizeC + c;\n    }\n    case 'XYCZT': {\n      return ({t, c, z}) => t * SizeC * SizeZ + z * SizeC + c;\n    }\n    case 'XYTCZ': {\n      return ({t, c, z}) => z * SizeT * SizeC + c * SizeT + t;\n    }\n    case 'XYTZC': {\n      return ({t, c, z}) => c * SizeT * SizeZ + z * SizeT + t;\n    }\n    default: {\n      throw new Error(`Invalid OME-XML DimensionOrder, got ${DimensionOrder}.`);\n    }\n  }\n}\n"],"file":"ome-indexers.js"}

package/dist/es5/lib/ome/ome-utils.js

@@ -1,18 +1,14 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.getOmePixelSourceMeta = getOmePixelSourceMeta;
 exports.DTYPE_LOOKUP = void 0;
 
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
 var _utils = require("./utils");
 
-var DTYPE_LOOKUP = {
+const DTYPE_LOOKUP = {
   uint8: 'Uint8',
   uint16: 'Uint16',
   uint32: 'Uint32',
@@ -24,11 +20,12 @@ var DTYPE_LOOKUP = {
 };
 exports.DTYPE_LOOKUP = DTYPE_LOOKUP;
 
-function getOmePixelSourceMeta(_ref) {
-  var Pixels = _ref.Pixels;
-  var labels = (0, _utils.getLabels)(Pixels.DimensionOrder);
-  var dims = (0, _utils.getDims)(labels);
-  var shape = Array(labels.length).fill(0);
+function getOmePixelSourceMeta({
+  Pixels
+}) {
+  const labels = (0, _utils.getLabels)(Pixels.DimensionOrder);
+  const dims = (0, _utils.getDims)(labels);
+  const shape = Array(labels.length).fill(0);
   shape[dims('t')] = Pixels.SizeT;
   shape[dims('c')] = Pixels.SizeC;
   shape[dims('z')] = Pixels.SizeZ;
@@ -38,8 +35,8 @@ function getOmePixelSourceMeta(_ref) {
     shape.push(3);
   }
 
-  var getShape = function getShape(level) {
-    var s = (0, _toConsumableArray2.default)(shape);
+  const getShape = level => {
+    const s = [...shape];
     s[dims('x')] = Pixels.SizeX >> level;
     s[dims('y')] = Pixels.SizeY >> level;
     return s;
@@ -49,10 +46,10 @@ function getOmePixelSourceMeta(_ref) {
     throw Error("Pixel type ".concat(Pixels.Type, " not supported."));
   }
 
-  var dtype = DTYPE_LOOKUP[Pixels.Type];
+  const dtype = DTYPE_LOOKUP[Pixels.Type];
 
   if (Pixels.PhysicalSizeX && Pixels.PhysicalSizeY) {
-    var physicalSizes = {
+    const physicalSizes = {
       x: {
         size: Pixels.PhysicalSizeX,
         unit: Pixels.PhysicalSizeXUnit
@@ -71,17 +68,17 @@ function getOmePixelSourceMeta(_ref) {
     }
 
     return {
-      labels: labels,
-      getShape: getShape,
-      physicalSizes: physicalSizes,
-      dtype: dtype
+      labels,
+      getShape,
+      physicalSizes,
+      dtype
     };
   }
 
   return {
-    labels: labels,
-    getShape: getShape,
-    dtype: dtype
+    labels,
+    getShape,
+    dtype
   };
 }
 //# sourceMappingURL=ome-utils.js.map

package/dist/es5/lib/ome/ome-utils.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../../../../src/lib/ome/ome-utils.ts"],"names":["DTYPE_LOOKUP","uint8","uint16","uint32","float","double","int8","int16","int32","getOmePixelSourceMeta","Pixels","labels","DimensionOrder","dims","shape","Array","length","fill","SizeT","SizeC","SizeZ","Interleaved","push","getShape","level","s","SizeX","SizeY","Type","Error","dtype","PhysicalSizeX","PhysicalSizeY","physicalSizes","x","size","unit","PhysicalSizeXUnit","y","PhysicalSizeYUnit","PhysicalSizeZ","z","PhysicalSizeZUnit"],"mappings":";;;;;;;;;;;;AAAA;;AAGO,IAAMA,YAAY,GAAG;AAC1BC,EAAAA,KAAK,EAAE,OADmB;AAE1BC,EAAAA,MAAM,EAAE,QAFkB;AAG1BC,EAAAA,MAAM,EAAE,QAHkB;AAI1BC,EAAAA,KAAK,EAAE,SAJmB;AAK1BC,EAAAA,MAAM,EAAE,SALkB;AAM1BC,EAAAA,IAAI,EAAE,MANoB;AAO1BC,EAAAA,KAAK,EAAE,OAPmB;AAQ1BC,EAAAA,KAAK,EAAE;AARmB,CAArB;;;AAWA,SAASC,qBAAT,OAAoD;AAAA,MAApBC,MAAoB,QAApBA,MAAoB;AAEzD,MAAMC,MAAM,GAAG,sBAAUD,MAAM,CAACE,cAAjB,CAAf;AAGA,MAAMC,IAAI,GAAG,oBAAQF,MAAR,CAAb;AACA,MAAMG,KAAe,GAAGC,KAAK,CAACJ,MAAM,CAACK,MAAR,CAAL,CAAqBC,IAArB,CAA0B,CAA1B,CAAxB;AACAH,EAAAA,KAAK,CAACD,IAAI,CAAC,GAAD,CAAL,CAAL,GAAmBH,MAAM,CAACQ,KAA1B;AACAJ,EAAAA,KAAK,CAACD,IAAI,CAAC,GAAD,CAAL,CAAL,GAAmBH,MAAM,CAACS,KAA1B;AACAL,EAAAA,KAAK,CAACD,IAAI,CAAC,GAAD,CAAL,CAAL,GAAmBH,MAAM,CAACU,KAA1B;;AAGA,MAAIV,MAAM,CAACW,WAAX,EAAwB;AAEtBV,IAAAA,MAAM,CAACW,IAAP,CAAY,IAAZ;AACAR,IAAAA,KAAK,CAACQ,IAAN,CAAW,CAAX;AACD;;AAID,MAAMC,QAAQ,GAAG,SAAXA,QAAW,CAACC,KAAD,EAAmB;AAClC,QAAMC,CAAC,oCAAOX,KAAP,CAAP;AACAW,IAAAA,CAAC,CAACZ,IAAI,CAAC,GAAD,CAAL,CAAD,GAAeH,MAAM,CAACgB,KAAP,IAAgBF,KAA/B;AACAC,IAAAA,CAAC,CAACZ,IAAI,CAAC,GAAD,CAAL,CAAD,GAAeH,MAAM,CAACiB,KAAP,IAAgBH,KAA/B;AACA,WAAOC,CAAP;AACD,GALD;;AAOA,MAAI,EAAEf,MAAM,CAACkB,IAAP,IAAe5B,YAAjB,CAAJ,EAAoC;AAClC,UAAM6B,KAAK,sBAAenB,MAAM,CAACkB,IAAtB,qBAAX;AACD;;AAED,MAAME,KAAK,GAAG9B,YAAY,CAACU,MAAM,CAACkB,IAAR,CAA1B;;AACA,MAAIlB,MAAM,CAACqB,aAAP,IAAwBrB,MAAM,CAACsB,aAAnC,EAAkD;AAChD,QAAMC,aAEL,GAAG;AACFC,MAAAA,CAAC,EAAE;AACDC,QAAAA,IAAI,EAAEzB,MAAM,CAACqB,aADZ;AAEDK,QAAAA,IAAI,EAAE1B,MAAM,CAAC2B;AAFZ,OADD;AAKFC,MAAAA,CAAC,EAAE;AACDH,QAAAA,IAAI,EAAEzB,MAAM,CAACsB,aADZ;AAEDI,QAAAA,IAAI,EAAE1B,MAAM,CAAC6B;AAFZ;AALD,KAFJ;;AAYA,QAAI7B,MAAM,CAAC8B,aAAX,EAA0B;AACxBP,MAAAA,aAAa,CAACQ,CAAd,GAAkB;AAChBN,QAAAA,IAAI,EAAEzB,MAAM,CAAC8B,aADG;AAEhBJ,QAAAA,IAAI,EAAE1B,MAAM,CAACgC;AAFG,OAAlB;AAID;;AACD,WAAO;AAAC/B,MAAAA,MAAM,EAANA,MAAD;AAASY,MAAAA,QAAQ,EAARA,QAAT;AAAmBU,MAAAA,aAAa,EAAbA,aAAnB;AAAkCH,MAAAA,KAAK,EAALA;AAAlC,KAAP;AACD;;AAED,SAAO;AAACnB,IAAAA,MAAM,EAANA,MAAD;AAASY,IAAAA,QAAQ,EAARA,QAAT;AAAmBO,IAAAA,KAAK,EAALA;AAAnB,GAAP;AACD","sourcesContent":["import {getDims, getLabels} from './utils';\nimport type {OMEXML, UnitsLength} from './omexml';\n\nexport const DTYPE_LOOKUP = {\n  uint8: 'Uint8',\n  uint16: 'Uint16',\n  uint32: 'Uint32',\n  float: 'Float32',\n  double: 'Float64',\n  int8: 'Int8',\n  int16: 'Int16',\n  int32: 'Int32'\n} as const;\n\nexport function getOmePixelSourceMeta({Pixels}: OMEXML[0]) {\n  // e.g. 'XYZCT' -> ['t', 'c', 'z', 'y', 'x']\n  const labels = getLabels(Pixels.DimensionOrder);\n\n  // Compute \"shape\" of image\n  const dims = getDims(labels);\n  const shape: number[] = Array(labels.length).fill(0);\n  shape[dims('t')] = Pixels.SizeT;\n  shape[dims('c')] = Pixels.SizeC;\n  shape[dims('z')] = Pixels.SizeZ;\n\n  // Push extra dimension if data are interleaved.\n  if (Pixels.Interleaved) {\n    // @ts-ignore\n    labels.push('_c');\n    shape.push(3);\n  }\n\n  // Creates a new shape for different level of pyramid.\n  // Assumes factor-of-two downsampling.\n  const getShape = (level: number) => {\n    const s = [...shape];\n    s[dims('x')] = Pixels.SizeX >> level;\n    s[dims('y')] = Pixels.SizeY >> level;\n    return s;\n  };\n\n  if (!(Pixels.Type in DTYPE_LOOKUP)) {\n    throw Error(`Pixel type ${Pixels.Type} not supported.`);\n  }\n\n  const dtype = DTYPE_LOOKUP[Pixels.Type as keyof typeof DTYPE_LOOKUP];\n  if (Pixels.PhysicalSizeX && Pixels.PhysicalSizeY) {\n    const physicalSizes: {\n      [k: string]: {size: number; unit: UnitsLength};\n    } = {\n      x: {\n        size: Pixels.PhysicalSizeX,\n        unit: Pixels.PhysicalSizeXUnit\n      },\n      y: {\n        size: Pixels.PhysicalSizeY,\n        unit: Pixels.PhysicalSizeYUnit\n      }\n    };\n    if (Pixels.PhysicalSizeZ) {\n      physicalSizes.z = {\n        size: Pixels.PhysicalSizeZ,\n        unit: Pixels.PhysicalSizeZUnit\n      };\n    }\n    return {labels, getShape, physicalSizes, dtype};\n  }\n\n  return {labels, getShape, dtype};\n}\n"],"file":"ome-utils.js"}
+{"version":3,"sources":["../../../../src/lib/ome/ome-utils.ts"],"names":["DTYPE_LOOKUP","uint8","uint16","uint32","float","double","int8","int16","int32","getOmePixelSourceMeta","Pixels","labels","DimensionOrder","dims","shape","Array","length","fill","SizeT","SizeC","SizeZ","Interleaved","push","getShape","level","s","SizeX","SizeY","Type","Error","dtype","PhysicalSizeX","PhysicalSizeY","physicalSizes","x","size","unit","PhysicalSizeXUnit","y","PhysicalSizeYUnit","PhysicalSizeZ","z","PhysicalSizeZUnit"],"mappings":";;;;;;;;AAAA;;AAGO,MAAMA,YAAY,GAAG;AAC1BC,EAAAA,KAAK,EAAE,OADmB;AAE1BC,EAAAA,MAAM,EAAE,QAFkB;AAG1BC,EAAAA,MAAM,EAAE,QAHkB;AAI1BC,EAAAA,KAAK,EAAE,SAJmB;AAK1BC,EAAAA,MAAM,EAAE,SALkB;AAM1BC,EAAAA,IAAI,EAAE,MANoB;AAO1BC,EAAAA,KAAK,EAAE,OAPmB;AAQ1BC,EAAAA,KAAK,EAAE;AARmB,CAArB;;;AAWA,SAASC,qBAAT,CAA+B;AAACC,EAAAA;AAAD,CAA/B,EAAoD;AAEzD,QAAMC,MAAM,GAAG,sBAAUD,MAAM,CAACE,cAAjB,CAAf;AAGA,QAAMC,IAAI,GAAG,oBAAQF,MAAR,CAAb;AACA,QAAMG,KAAe,GAAGC,KAAK,CAACJ,MAAM,CAACK,MAAR,CAAL,CAAqBC,IAArB,CAA0B,CAA1B,CAAxB;AACAH,EAAAA,KAAK,CAACD,IAAI,CAAC,GAAD,CAAL,CAAL,GAAmBH,MAAM,CAACQ,KAA1B;AACAJ,EAAAA,KAAK,CAACD,IAAI,CAAC,GAAD,CAAL,CAAL,GAAmBH,MAAM,CAACS,KAA1B;AACAL,EAAAA,KAAK,CAACD,IAAI,CAAC,GAAD,CAAL,CAAL,GAAmBH,MAAM,CAACU,KAA1B;;AAGA,MAAIV,MAAM,CAACW,WAAX,EAAwB;AAEtBV,IAAAA,MAAM,CAACW,IAAP,CAAY,IAAZ;AACAR,IAAAA,KAAK,CAACQ,IAAN,CAAW,CAAX;AACD;;AAID,QAAMC,QAAQ,GAAIC,KAAD,IAAmB;AAClC,UAAMC,CAAC,GAAG,CAAC,GAAGX,KAAJ,CAAV;AACAW,IAAAA,CAAC,CAACZ,IAAI,CAAC,GAAD,CAAL,CAAD,GAAeH,MAAM,CAACgB,KAAP,IAAgBF,KAA/B;AACAC,IAAAA,CAAC,CAACZ,IAAI,CAAC,GAAD,CAAL,CAAD,GAAeH,MAAM,CAACiB,KAAP,IAAgBH,KAA/B;AACA,WAAOC,CAAP;AACD,GALD;;AAOA,MAAI,EAAEf,MAAM,CAACkB,IAAP,IAAe5B,YAAjB,CAAJ,EAAoC;AAClC,UAAM6B,KAAK,sBAAenB,MAAM,CAACkB,IAAtB,qBAAX;AACD;;AAED,QAAME,KAAK,GAAG9B,YAAY,CAACU,MAAM,CAACkB,IAAR,CAA1B;;AACA,MAAIlB,MAAM,CAACqB,aAAP,IAAwBrB,MAAM,CAACsB,aAAnC,EAAkD;AAChD,UAAMC,aAEL,GAAG;AACFC,MAAAA,CAAC,EAAE;AACDC,QAAAA,IAAI,EAAEzB,MAAM,CAACqB,aADZ;AAEDK,QAAAA,IAAI,EAAE1B,MAAM,CAAC2B;AAFZ,OADD;AAKFC,MAAAA,CAAC,EAAE;AACDH,QAAAA,IAAI,EAAEzB,MAAM,CAACsB,aADZ;AAEDI,QAAAA,IAAI,EAAE1B,MAAM,CAAC6B;AAFZ;AALD,KAFJ;;AAYA,QAAI7B,MAAM,CAAC8B,aAAX,EAA0B;AACxBP,MAAAA,aAAa,CAACQ,CAAd,GAAkB;AAChBN,QAAAA,IAAI,EAAEzB,MAAM,CAAC8B,aADG;AAEhBJ,QAAAA,IAAI,EAAE1B,MAAM,CAACgC;AAFG,OAAlB;AAID;;AACD,WAAO;AAAC/B,MAAAA,MAAD;AAASY,MAAAA,QAAT;AAAmBU,MAAAA,aAAnB;AAAkCH,MAAAA;AAAlC,KAAP;AACD;;AAED,SAAO;AAACnB,IAAAA,MAAD;AAASY,IAAAA,QAAT;AAAmBO,IAAAA;AAAnB,GAAP;AACD","sourcesContent":["import {getDims, getLabels} from './utils';\nimport type {OMEXML, UnitsLength} from './omexml';\n\nexport const DTYPE_LOOKUP = {\n  uint8: 'Uint8',\n  uint16: 'Uint16',\n  uint32: 'Uint32',\n  float: 'Float32',\n  double: 'Float64',\n  int8: 'Int8',\n  int16: 'Int16',\n  int32: 'Int32'\n} as const;\n\nexport function getOmePixelSourceMeta({Pixels}: OMEXML[0]) {\n  // e.g. 'XYZCT' -> ['t', 'c', 'z', 'y', 'x']\n  const labels = getLabels(Pixels.DimensionOrder);\n\n  // Compute \"shape\" of image\n  const dims = getDims(labels);\n  const shape: number[] = Array(labels.length).fill(0);\n  shape[dims('t')] = Pixels.SizeT;\n  shape[dims('c')] = Pixels.SizeC;\n  shape[dims('z')] = Pixels.SizeZ;\n\n  // Push extra dimension if data are interleaved.\n  if (Pixels.Interleaved) {\n    // @ts-ignore\n    labels.push('_c');\n    shape.push(3);\n  }\n\n  // Creates a new shape for different level of pyramid.\n  // Assumes factor-of-two downsampling.\n  const getShape = (level: number) => {\n    const s = [...shape];\n    s[dims('x')] = Pixels.SizeX >> level;\n    s[dims('y')] = Pixels.SizeY >> level;\n    return s;\n  };\n\n  if (!(Pixels.Type in DTYPE_LOOKUP)) {\n    throw Error(`Pixel type ${Pixels.Type} not supported.`);\n  }\n\n  const dtype = DTYPE_LOOKUP[Pixels.Type as keyof typeof DTYPE_LOOKUP];\n  if (Pixels.PhysicalSizeX && Pixels.PhysicalSizeY) {\n    const physicalSizes: {\n      [k: string]: {size: number; unit: UnitsLength};\n    } = {\n      x: {\n        size: Pixels.PhysicalSizeX,\n        unit: Pixels.PhysicalSizeXUnit\n      },\n      y: {\n        size: Pixels.PhysicalSizeY,\n        unit: Pixels.PhysicalSizeYUnit\n      }\n    };\n    if (Pixels.PhysicalSizeZ) {\n      physicalSizes.z = {\n        size: Pixels.PhysicalSizeZ,\n        unit: Pixels.PhysicalSizeZUnit\n      };\n    }\n    return {labels, getShape, physicalSizes, dtype};\n  }\n\n  return {labels, getShape, dtype};\n}\n"],"file":"ome-utils.js"}

package/dist/es5/lib/ome/omexml.js

@@ -7,17 +7,11 @@ Object.defineProperty(exports, "__esModule", {
 });
 exports.fromString = fromString;
 
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
 var _fastXmlParser = _interopRequireDefault(require("fast-xml-parser"));
 
 var _tiffUtils = require("../utils/tiff-utils");
 
-function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); if (enumerableOnly) { symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; }); } keys.push.apply(keys, symbols); } return keys; }
-
-function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = arguments[i] != null ? arguments[i] : {}; if (i % 2) { ownKeys(Object(source), true).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }); } else if (Object.getOwnPropertyDescriptors) { Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)); } else { ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } } return target; }
-
-var PARSER_OPTIONS = {
+const PARSER_OPTIONS = {
   attributeNamePrefix: '',
   attrNodeName: 'attr',
   parseNodeValue: true,
@@ -25,46 +19,46 @@ var PARSER_OPTIONS = {
   ignoreAttributes: false
 };
 
-var parse = function parse(str) {
-  return _fastXmlParser.default.parse(str, PARSER_OPTIONS);
-};
+const parse = str => _fastXmlParser.default.parse(str, PARSER_OPTIONS);
 
 function fromString(str) {
-  var res = parse(str);
+  const res = parse(str);
 
   if (!res.OME) {
     throw Error('Failed to parse OME-XML metadata.');
   }
 
-  return (0, _tiffUtils.ensureArray)(res.OME.Image).map(function (img) {
-    var Channels = (0, _tiffUtils.ensureArray)(img.Pixels.Channel).map(function (c) {
+  return (0, _tiffUtils.ensureArray)(res.OME.Image).map(img => {
+    const Channels = (0, _tiffUtils.ensureArray)(img.Pixels.Channel).map(c => {
       if ('Color' in c.attr) {
-        return _objectSpread(_objectSpread({}, c.attr), {}, {
+        return { ...c.attr,
           Color: (0, _tiffUtils.intToRgba)(c.attr.Color)
-        });
+        };
       }
 
-      return _objectSpread({}, c.attr);
-    });
-    var _img$AquisitionDate = img.AquisitionDate,
-        AquisitionDate = _img$AquisitionDate === void 0 ? '' : _img$AquisitionDate,
-        _img$Description = img.Description,
-        Description = _img$Description === void 0 ? '' : _img$Description;
-
-    var image = _objectSpread(_objectSpread({}, img.attr), {}, {
-      AquisitionDate: AquisitionDate,
-      Description: Description,
-      Pixels: _objectSpread(_objectSpread({}, img.Pixels.attr), {}, {
-        Channels: Channels
-      })
+      return { ...c.attr
+      };
     });
+    const {
+      AquisitionDate = '',
+      Description = ''
+    } = img;
+    const image = { ...img.attr,
+      AquisitionDate,
+      Description,
+      Pixels: { ...img.Pixels.attr,
+        Channels
+      }
+    };
+    return { ...image,
 
-    return _objectSpread(_objectSpread({}, image), {}, {
-      format: function format() {
-        var Pixels = image.Pixels;
-        var sizes = ['X', 'Y', 'Z'].map(function (name) {
-          var size = Pixels["PhysicalSize".concat(name)];
-          var unit = Pixels["PhysicalSize".concat(name, "Unit")];
+      format() {
+        const {
+          Pixels
+        } = image;
+        const sizes = ['X', 'Y', 'Z'].map(name => {
+          const size = Pixels["PhysicalSize".concat(name)];
+          const unit = Pixels["PhysicalSize".concat(name, "Unit")];
           return size && unit ? "".concat(size, " ").concat(unit) : '-';
         }).join(' x ');
         return {
@@ -76,7 +70,8 @@ function fromString(str) {
           Channels: Pixels.SizeC
         };
       }
-    });
+
+    };
   });
 }
 //# sourceMappingURL=omexml.js.map

package/dist/es5/lib/ome/omexml.js.map

@@ -1 +1 @@
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`${size} ${unit}` : '-';\n          })\n          .join(' x ');\n\n        return {\n          'Acquisition Date': image.AquisitionDate,\n          'Dimensions (XY)': `${Pixels.SizeX} x ${Pixels.SizeY}`,\n          'Pixels Type': Pixels.Type,\n          'Pixels Size (XYZ)': sizes,\n          'Z-sections/Timepoints': `${Pixels.SizeZ} x ${Pixels.SizeT}`,\n          Channels: Pixels.SizeC\n        };\n      }\n    };\n  });\n}\n\nexport type OMEXML = ReturnType<typeof fromString>;\nexport type DimensionOrder = 'XYZCT' | 'XYZTC' | 'XYCTZ' | 'XYCZT' | 'XYTCZ' | 'XYTZC';\n\n// Structure of node is determined by the PARSER_OPTIONS.\ntype Node<T, A> = T & {attr: A};\ntype Attrs<Fields extends string, T = string> = {[K in Fields]: T};\n\ntype OMEAttrs = Attrs<'xmlns' | 'xmlns:xsi' | 'xsi:schemaLocation'>;\ntype OME = Node<{Insturment: Insturment; Image: Image | Image[]}, OMEAttrs>;\n\ntype Insturment = Node<\n  {Objective: Node<{}, Attrs<'ID' | 'Model' | 'NominalMagnification'>>},\n  Attrs<'ID'>\n>;\n\ninterface ImageNodes {\n  AquisitionDate?: string;\n  Description?: string;\n  Pixels: Pixels;\n  InstrumentRef: Node<{}, {ID: string}>;\n  ObjectiveSettings: Node<{}, {ID: string}>;\n}\ntype Image = Node<ImageNodes, Attrs<'ID' | 'Name'>>;\n\ntype PixelType =\n  | 'int8'\n  | 'int16'\n  | 'int32'\n  | 'uint8'\n  | 'uint16'\n  | 'uint32'\n  | 'float'\n  | 'bit'\n  | 'double'\n  | 'complex'\n  | 'double-complex';\n\nexport type UnitsLength =\n  | 'Ym'\n  | 'Zm'\n  | 'Em'\n  | 'Pm'\n  | 'Tm'\n  | 'Gm'\n  | 'Mm'\n  | 'km'\n  | 'hm'\n  | 'dam'\n  | 'm'\n  | 'dm'\n  | 'cm'\n  | 'mm'\n  | 'µm'\n  | 'nm'\n  | 'pm'\n  | 'fm'\n  | 'am'\n  | 'zm'\n  | 'ym'\n  | 'Å'\n  | 'thou'\n  | 'li'\n  | 'in'\n  | 'ft'\n  | 'yd'\n  | 'mi'\n  | 'ua'\n  | 'ly'\n  | 'pc'\n  | 'pt'\n  | 'pixel'\n  | 'reference frame';\n\ntype PhysicalSize<Name extends string> = `PhysicalSize${Name}`;\ntype PhysicalSizeUnit<Name extends string> = `PhysicalSize${Name}Unit`;\ntype Size<Names extends string> = `Size${Names}`;\n\ntype PixelAttrs = Attrs<\n  PhysicalSize<'X' | 'Y' | 'Z'> | 'SignificantBits' | Size<'T' | 'C' | 'Z' | 'Y' | 'X'>,\n  number\n> &\n  Attrs<PhysicalSizeUnit<'X' | 'Y' | 'Z'>, UnitsLength> &\n  Attrs<'BigEndian' | 'Interleaved', boolean> & {\n    ID: string;\n    DimensionOrder: DimensionOrder;\n    Type: PixelType;\n  };\n\ntype Pixels = Node<\n  {\n    Channel: Channel | Channel[];\n    TiffData: Node<{}, Attrs<'IFD' | 'PlaneCount'>>;\n  },\n  PixelAttrs\n>;\n\ntype ChannelAttrs =\n  | {\n      ID: string;\n      SamplesPerPixel: number;\n      Name?: string;\n    }\n  | {\n      ID: string;\n      SamplesPerPixel: number;\n      Name?: string;\n      Color: number;\n    };\n\ntype Channel = Node<{}, ChannelAttrs>;\n\ntype Root = {OME: OME};\n"],"file":"omexml.js"}
+{"version":3,"sources":["../../../../src/lib/ome/omexml.ts"],"names":["PARSER_OPTIONS","attributeNamePrefix","attrNodeName","parseNodeValue","parseAttributeValue","ignoreAttributes","parse","str","parser","fromString","res","OME","Error","Image","map","img","Channels","Pixels","Channel","c","attr","Color","AquisitionDate","Description","image","format","sizes","name","size","unit","join","SizeX","SizeY","Type","SizeZ","SizeT","SizeC"],"mappings":";;;;;;;;;AAAA;;AACA;;AAGA,MAAMA,cAAc,GAAG;AAErBC,EAAAA,mBAAmB,EAAE,EAFA;AAGrBC,EAAAA,YAAY,EAAE,MAHO;AAMrBC,EAAAA,cAAc,EAAE,IANK;AAOrBC,EAAAA,mBAAmB,EAAE,IAPA;AAUrBC,EAAAA,gBAAgB,EAAE;AAVG,CAAvB;;AAaA,MAAMC,KAAK,GAAIC,GAAD,IAAuBC,uBAAOF,KAAP,CAAaC,GAAb,EAAkBP,cAAlB,CAArC;;AAEO,SAASS,UAAT,CAAoBF,GAApB,EAAiC;AACtC,QAAMG,GAAG,GAAGJ,KAAK,CAACC,GAAD,CAAjB;;AACA,MAAI,CAACG,GAAG,CAACC,GAAT,EAAc;AACZ,UAAMC,KAAK,CAAC,mCAAD,CAAX;AACD;;AACD,SAAO,4BAAYF,GAAG,CAACC,GAAJ,CAAQE,KAApB,EAA2BC,GAA3B,CAAgCC,GAAD,IAAS;AAC7C,UAAMC,QAAQ,GAAG,4BAAYD,GAAG,CAACE,MAAJ,CAAWC,OAAvB,EAAgCJ,GAAhC,CAAqCK,CAAD,IAAO;AAC1D,UAAI,WAAWA,CAAC,CAACC,IAAjB,EAAuB;AACrB,eAAO,EAAC,GAAGD,CAAC,CAACC,IAAN;AAAYC,UAAAA,KAAK,EAAE,0BAAUF,CAAC,CAACC,IAAF,CAAOC,KAAjB;AAAnB,SAAP;AACD;;AACD,aAAO,EAAC,GAAGF,CAAC,CAACC;AAAN,OAAP;AACD,KALgB,CAAjB;AAMA,UAAM;AAACE,MAAAA,cAAc,GAAG,EAAlB;AAAsBC,MAAAA,WAAW,GAAG;AAApC,QAA0CR,GAAhD;AACA,UAAMS,KAAK,GAAG,EACZ,GAAGT,GAAG,CAACK,IADK;AAEZE,MAAAA,cAFY;AAGZC,MAAAA,WAHY;AAIZN,MAAAA,MAAM,EAAE,EACN,GAAGF,GAAG,CAACE,MAAJ,CAAWG,IADR;AAENJ,QAAAA;AAFM;AAJI,KAAd;AASA,WAAO,EACL,GAAGQ,KADE;;AAELC,MAAAA,MAAM,GAAG;AACP,cAAM;AAACR,UAAAA;AAAD,YAAWO,KAAjB;AAEA,cAAME,KAAK,GAAI,CAAC,GAAD,EAAM,GAAN,EAAW,GAAX,CAAD,CACXZ,GADW,CACNa,IAAD,IAAU;AACb,gBAAMC,IAAI,GAAGX,MAAM,uBAAgBU,IAAhB,EAAnB;AACA,gBAAME,IAAI,GAAGZ,MAAM,uBAAgBU,IAAhB,UAAnB;AACA,iBAAOC,IAAI,IAAIC,IAAR,aAAkBD,IAAlB,cAA0BC,IAA1B,IAAmC,GAA1C;AACD,SALW,EAMXC,IANW,CAMN,KANM,CAAd;AAQA,eAAO;AACL,8BAAoBN,KAAK,CAACF,cADrB;AAEL,uCAAsBL,MAAM,CAACc,KAA7B,gBAAwCd,MAAM,CAACe,KAA/C,CAFK;AAGL,yBAAef,MAAM,CAACgB,IAHjB;AAIL,+BAAqBP,KAJhB;AAKL,6CAA4BT,MAAM,CAACiB,KAAnC,gBAA8CjB,MAAM,CAACkB,KAArD,CALK;AAMLnB,UAAAA,QAAQ,EAAEC,MAAM,CAACmB;AANZ,SAAP;AAQD;;AArBI,KAAP;AAuBD,GAxCM,CAAP;AAyCD","sourcesContent":["import parser from 'fast-xml-parser';\nimport {ensureArray, intToRgba} from '../utils/tiff-utils';\n\n// WARNING: Changes to the parser options _will_ effect the types in types/omexml.d.ts.\nconst PARSER_OPTIONS = {\n  // Nests attributes withtout prefix under 'attr' key for each node\n  attributeNamePrefix: '',\n  attrNodeName: 'attr',\n\n  // Parses numbers for both attributes and nodes\n  parseNodeValue: true,\n  parseAttributeValue: true,\n\n  // Forces attributes to be parsed\n  ignoreAttributes: false\n};\n\nconst parse = (str: string): Root => parser.parse(str, PARSER_OPTIONS);\n\nexport function fromString(str: string) {\n  const res = parse(str);\n  if (!res.OME) {\n    throw Error('Failed to parse OME-XML metadata.');\n  }\n  return ensureArray(res.OME.Image).map((img) => {\n    const Channels = ensureArray(img.Pixels.Channel).map((c) => {\n      if ('Color' in c.attr) {\n        return {...c.attr, Color: intToRgba(c.attr.Color)};\n      }\n      return {...c.attr};\n    });\n    const {AquisitionDate = '', Description = ''} = img;\n    const image = {\n      ...img.attr,\n      AquisitionDate,\n      Description,\n      Pixels: {\n        ...img.Pixels.attr,\n        Channels\n      }\n    };\n    return {\n      ...image,\n      format() {\n        const {Pixels} = image;\n\n        const sizes = (['X', 'Y', 'Z'] as const)\n          .map((name) => {\n            const size = Pixels[`PhysicalSize${name}` as const];\n            const unit = Pixels[`PhysicalSize${name}Unit` as const];\n            return size && unit ? `${size} ${unit}` : '-';\n          })\n          .join(' x ');\n\n        return {\n          'Acquisition Date': image.AquisitionDate,\n          'Dimensions (XY)': `${Pixels.SizeX} x ${Pixels.SizeY}`,\n          'Pixels Type': Pixels.Type,\n          'Pixels Size (XYZ)': sizes,\n          'Z-sections/Timepoints': `${Pixels.SizeZ} x ${Pixels.SizeT}`,\n          Channels: Pixels.SizeC\n        };\n      }\n    };\n  });\n}\n\nexport type OMEXML = ReturnType<typeof fromString>;\nexport type DimensionOrder = 'XYZCT' | 'XYZTC' | 'XYCTZ' | 'XYCZT' | 'XYTCZ' | 'XYTZC';\n\n// Structure of node is determined by the PARSER_OPTIONS.\ntype Node<T, A> = T & {attr: A};\ntype Attrs<Fields extends string, T = string> = {[K in Fields]: T};\n\ntype OMEAttrs = Attrs<'xmlns' | 'xmlns:xsi' | 'xsi:schemaLocation'>;\ntype OME = Node<{Insturment: Insturment; Image: Image | Image[]}, OMEAttrs>;\n\ntype Insturment = Node<\n  {Objective: Node<{}, Attrs<'ID' | 'Model' | 'NominalMagnification'>>},\n  Attrs<'ID'>\n>;\n\ninterface ImageNodes {\n  AquisitionDate?: string;\n  Description?: string;\n  Pixels: Pixels;\n  InstrumentRef: Node<{}, {ID: string}>;\n  ObjectiveSettings: Node<{}, {ID: string}>;\n}\ntype Image = Node<ImageNodes, Attrs<'ID' | 'Name'>>;\n\ntype PixelType =\n  | 'int8'\n  | 'int16'\n  | 'int32'\n  | 'uint8'\n  | 'uint16'\n  | 'uint32'\n  | 'float'\n  | 'bit'\n  | 'double'\n  | 'complex'\n  | 'double-complex';\n\nexport type UnitsLength =\n  | 'Ym'\n  | 'Zm'\n  | 'Em'\n  | 'Pm'\n  | 'Tm'\n  | 'Gm'\n  | 'Mm'\n  | 'km'\n  | 'hm'\n  | 'dam'\n  | 'm'\n  | 'dm'\n  | 'cm'\n  | 'mm'\n  | 'µm'\n  | 'nm'\n  | 'pm'\n  | 'fm'\n  | 'am'\n  | 'zm'\n  | 'ym'\n  | 'Å'\n  | 'thou'\n  | 'li'\n  | 'in'\n  | 'ft'\n  | 'yd'\n  | 'mi'\n  | 'ua'\n  | 'ly'\n  | 'pc'\n  | 'pt'\n  | 'pixel'\n  | 'reference frame';\n\ntype PhysicalSize<Name extends string> = `PhysicalSize${Name}`;\ntype PhysicalSizeUnit<Name extends string> = `PhysicalSize${Name}Unit`;\ntype Size<Names extends string> = `Size${Names}`;\n\ntype PixelAttrs = Attrs<\n  PhysicalSize<'X' | 'Y' | 'Z'> | 'SignificantBits' | Size<'T' | 'C' | 'Z' | 'Y' | 'X'>,\n  number\n> &\n  Attrs<PhysicalSizeUnit<'X' | 'Y' | 'Z'>, UnitsLength> &\n  Attrs<'BigEndian' | 'Interleaved', boolean> & {\n    ID: string;\n    DimensionOrder: DimensionOrder;\n    Type: PixelType;\n  };\n\ntype Pixels = Node<\n  {\n    Channel: Channel | Channel[];\n    TiffData: Node<{}, Attrs<'IFD' | 'PlaneCount'>>;\n  },\n  PixelAttrs\n>;\n\ntype ChannelAttrs =\n  | {\n      ID: string;\n      SamplesPerPixel: number;\n      Name?: string;\n    }\n  | {\n      ID: string;\n      SamplesPerPixel: number;\n      Name?: string;\n      Color: number;\n    };\n\ntype Channel = Node<{}, ChannelAttrs>;\n\ntype Root = {OME: OME};\n"],"file":"omexml.js"}

package/dist/es5/lib/ome/utils.js

@@ -11,16 +11,14 @@ function getLabels(dimOrder) {
 }
 
 function getDims(labels) {
-  var lookup = new Map(labels.map(function (name, i) {
-    return [name, i];
-  }));
+  const lookup = new Map(labels.map((name, i) => [name, i]));
 
   if (lookup.size !== labels.length) {
     throw Error('Labels must be unique, found duplicated label.');
   }
 
-  return function (name) {
-    var index = lookup.get(name);
+  return name => {
+    const index = lookup.get(name);
 
     if (index === undefined) {
       throw Error('Invalid dimension.');

package/dist/es5/lib/ome/utils.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../../../../src/lib/ome/utils.ts"],"names":["getLabels","dimOrder","toLowerCase","split","reverse","getDims","labels","lookup","Map","map","name","i","size","length","Error","index","get","undefined"],"mappings":";;;;;;;;AAaO,SAASA,SAAT,CAAmBC,QAAnB,EAAoE;AACzE,SAAOA,QAAQ,CAACC,WAAT,GAAuBC,KAAvB,CAA6B,EAA7B,EAAiCC,OAAjC,EAAP;AACD;;AAWM,SAASC,OAAT,CAAmCC,MAAnC,EAAgD;AACrD,MAAMC,MAAM,GAAG,IAAIC,GAAJ,CAAQF,MAAM,CAACG,GAAP,CAAW,UAACC,IAAD,EAAOC,CAAP;AAAA,WAAa,CAACD,IAAD,EAAOC,CAAP,CAAb;AAAA,GAAX,CAAR,CAAf;;AACA,MAAIJ,MAAM,CAACK,IAAP,KAAgBN,MAAM,CAACO,MAA3B,EAAmC;AACjC,UAAMC,KAAK,CAAC,gDAAD,CAAX;AACD;;AACD,SAAO,UAACJ,IAAD,EAAa;AAClB,QAAMK,KAAK,GAAGR,MAAM,CAACS,GAAP,CAAWN,IAAX,CAAd;;AACA,QAAIK,KAAK,KAAKE,SAAd,EAAyB;AACvB,YAAMH,KAAK,CAAC,oBAAD,CAAX;AACD;;AACD,WAAOC,KAAP;AACD,GAND;AAOD","sourcesContent":["import type {OMEXML} from '../ome/omexml';\nimport type {Labels} from '../../types';\n\n/*\n * Creates typed labels from DimensionOrder.\n * > imgMeta.Pixels.DimensionOrder === 'XYCZT'\n * > getLabels(imgMeta.Pixels) === ['t', 'z', 'c', 'y', 'x']\n */\n\n// eslint-disable-next-line @typescript-eslint/no-unused-vars\ntype Sel<Dim extends string> = Dim extends `${infer Z}${infer X}${infer A}${infer B}${infer C}`\n  ? [C, B, A]\n  : 'error';\nexport function getLabels(dimOrder: OMEXML[0]['Pixels']['DimensionOrder']) {\n  return dimOrder.toLowerCase().split('').reverse() as Labels<Sel<Lowercase<typeof dimOrder>>>;\n}\n\n/*\n * Creates an ES6 map of 'label' -> index\n * > const labels = ['a', 'b', 'c', 'd'];\n * > const dims = getDims(labels);\n * > dims('a') === 0;\n * > dims('b') === 1;\n * > dims('c') === 2;\n * > dims('hi!'); // throws\n */\nexport function getDims<S extends string>(labels: S[]) {\n  const lookup = new Map(labels.map((name, i) => [name, i]));\n  if (lookup.size !== labels.length) {\n    throw Error('Labels must be unique, found duplicated label.');\n  }\n  return (name: S) => {\n    const index = lookup.get(name);\n    if (index === undefined) {\n      throw Error('Invalid dimension.');\n    }\n    return index;\n  };\n}\n"],"file":"utils.js"}
+{"version":3,"sources":["../../../../src/lib/ome/utils.ts"],"names":["getLabels","dimOrder","toLowerCase","split","reverse","getDims","labels","lookup","Map","map","name","i","size","length","Error","index","get","undefined"],"mappings":";;;;;;;;AAaO,SAASA,SAAT,CAAmBC,QAAnB,EAAoE;AACzE,SAAOA,QAAQ,CAACC,WAAT,GAAuBC,KAAvB,CAA6B,EAA7B,EAAiCC,OAAjC,EAAP;AACD;;AAWM,SAASC,OAAT,CAAmCC,MAAnC,EAAgD;AACrD,QAAMC,MAAM,GAAG,IAAIC,GAAJ,CAAQF,MAAM,CAACG,GAAP,CAAW,CAACC,IAAD,EAAOC,CAAP,KAAa,CAACD,IAAD,EAAOC,CAAP,CAAxB,CAAR,CAAf;;AACA,MAAIJ,MAAM,CAACK,IAAP,KAAgBN,MAAM,CAACO,MAA3B,EAAmC;AACjC,UAAMC,KAAK,CAAC,gDAAD,CAAX;AACD;;AACD,SAAQJ,IAAD,IAAa;AAClB,UAAMK,KAAK,GAAGR,MAAM,CAACS,GAAP,CAAWN,IAAX,CAAd;;AACA,QAAIK,KAAK,KAAKE,SAAd,EAAyB;AACvB,YAAMH,KAAK,CAAC,oBAAD,CAAX;AACD;;AACD,WAAOC,KAAP;AACD,GAND;AAOD","sourcesContent":["import type {OMEXML} from '../ome/omexml';\nimport type {Labels} from '../../types';\n\n/*\n * Creates typed labels from DimensionOrder.\n * > imgMeta.Pixels.DimensionOrder === 'XYCZT'\n * > getLabels(imgMeta.Pixels) === ['t', 'z', 'c', 'y', 'x']\n */\n\n// eslint-disable-next-line @typescript-eslint/no-unused-vars\ntype Sel<Dim extends string> = Dim extends `${infer Z}${infer X}${infer A}${infer B}${infer C}`\n  ? [C, B, A]\n  : 'error';\nexport function getLabels(dimOrder: OMEXML[0]['Pixels']['DimensionOrder']) {\n  return dimOrder.toLowerCase().split('').reverse() as Labels<Sel<Lowercase<typeof dimOrder>>>;\n}\n\n/*\n * Creates an ES6 map of 'label' -> index\n * > const labels = ['a', 'b', 'c', 'd'];\n * > const dims = getDims(labels);\n * > dims('a') === 0;\n * > dims('b') === 1;\n * > dims('c') === 2;\n * > dims('hi!'); // throws\n */\nexport function getDims<S extends string>(labels: S[]) {\n  const lookup = new Map(labels.map((name, i) => [name, i]));\n  if (lookup.size !== labels.length) {\n    throw Error('Labels must be unique, found duplicated label.');\n  }\n  return (name: S) => {\n    const index = lookup.get(name);\n    if (index === undefined) {\n      throw Error('Invalid dimension.');\n    }\n    return index;\n  };\n}\n"],"file":"utils.js"}

package/dist/es5/lib/tiff-pixel-source.js

@@ -7,25 +7,12 @@ Object.defineProperty(exports, "__esModule", {
 });
 exports.default = void 0;
 
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
-
 var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
 
 var _tiffUtils = require("./utils/tiff-utils");
 
-function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); if (enumerableOnly) { symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; }); } keys.push.apply(keys, symbols); } return keys; }
-
-function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = arguments[i] != null ? arguments[i] : {}; if (i % 2) { ownKeys(Object(source), true).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }); } else if (Object.getOwnPropertyDescriptors) { Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)); } else { ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } } return target; }
-
-var TiffPixelSource = function () {
-  function TiffPixelSource(indexer, dtype, tileSize, shape, labels, meta) {
-    (0, _classCallCheck2.default)(this, TiffPixelSource);
+class TiffPixelSource {
+  constructor(indexer, dtype, tileSize, shape, labels, meta) {
     (0, _defineProperty2.default)(this, "dtype", void 0);
     (0, _defineProperty2.default)(this, "tileSize", void 0);
     (0, _defineProperty2.default)(this, "shape", void 0);
@@ -40,162 +27,89 @@ var TiffPixelSource = function () {
     this.meta = meta;
   }
 
-  (0, _createClass2.default)(TiffPixelSource, [{
-    key: "getRaster",
-    value: function () {
-      var _getRaster = (0, _asyncToGenerator2.default)(_regenerator.default.mark(function _callee(_ref) {
-        var selection, signal, image;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                selection = _ref.selection, signal = _ref.signal;
-                _context.next = 3;
-                return this._indexer(selection);
-
-              case 3:
-                image = _context.sent;
-                return _context.abrupt("return", this._readRasters(image, {
-                  signal: signal
-                }));
-
-              case 5:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function getRaster(_x) {
-        return _getRaster.apply(this, arguments);
-      }
-
-      return getRaster;
-    }()
-  }, {
-    key: "getTile",
-    value: function () {
-      var _getTile = (0, _asyncToGenerator2.default)(_regenerator.default.mark(function _callee2(_ref2) {
-        var x, y, selection, signal, _this$_getTileExtent, height, width, x0, y0, window, image;
-
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                x = _ref2.x, y = _ref2.y, selection = _ref2.selection, signal = _ref2.signal;
-                _this$_getTileExtent = this._getTileExtent(x, y), height = _this$_getTileExtent.height, width = _this$_getTileExtent.width;
-                x0 = x * this.tileSize;
-                y0 = y * this.tileSize;
-                window = [x0, y0, x0 + width, y0 + height];
-                _context2.next = 7;
-                return this._indexer(selection);
-
-              case 7:
-                image = _context2.sent;
-                return _context2.abrupt("return", this._readRasters(image, {
-                  window: window,
-                  width: width,
-                  height: height,
-                  signal: signal
-                }));
-
-              case 9:
-              case "end":
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function getTile(_x2) {
-        return _getTile.apply(this, arguments);
-      }
-
-      return getTile;
-    }()
-  }, {
-    key: "_readRasters",
-    value: function () {
-      var _readRasters2 = (0, _asyncToGenerator2.default)(_regenerator.default.mark(function _callee3(image, props) {
-        var _props$signal;
-
-        var interleave, raster, data;
-        return _regenerator.default.wrap(function _callee3$(_context3) {
-          while (1) {
-            switch (_context3.prev = _context3.next) {
-              case 0:
-                interleave = (0, _tiffUtils.isInterleaved)(this.shape);
-                _context3.next = 3;
-                return image.readRasters(_objectSpread({
-                  interleave: interleave
-                }, props));
-
-              case 3:
-                raster = _context3.sent;
-
-                if (!(props !== null && props !== void 0 && (_props$signal = props.signal) !== null && _props$signal !== void 0 && _props$signal.aborted)) {
-                  _context3.next = 6;
-                  break;
-                }
-
-                throw _tiffUtils.SIGNAL_ABORTED;
-
-              case 6:
-                data = interleave ? raster : raster[0];
-                return _context3.abrupt("return", {
-                  data: data,
-                  width: raster.width,
-                  height: raster.height
-                });
-
-              case 8:
-              case "end":
-                return _context3.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
-
-      function _readRasters(_x3, _x4) {
-        return _readRasters2.apply(this, arguments);
-      }
-
-      return _readRasters;
-    }()
-  }, {
-    key: "_getTileExtent",
-    value: function _getTileExtent(x, y) {
-      var _getImageSize = (0, _tiffUtils.getImageSize)(this),
-          zoomLevelHeight = _getImageSize.height,
-          zoomLevelWidth = _getImageSize.width;
-
-      var height = this.tileSize;
-      var width = this.tileSize;
-      var maxXTileCoord = Math.floor(zoomLevelWidth / this.tileSize);
-      var maxYTileCoord = Math.floor(zoomLevelHeight / this.tileSize);
-
-      if (x === maxXTileCoord) {
-        width = zoomLevelWidth % this.tileSize;
-      }
-
-      if (y === maxYTileCoord) {
-        height = zoomLevelHeight % this.tileSize;
-      }
-
-      return {
-        height: height,
-        width: width
-      };
+  async getRaster({
+    selection,
+    signal
+  }) {
+    const image = await this._indexer(selection);
+    return this._readRasters(image, {
+      signal
+    });
+  }
+
+  async getTile({
+    x,
+    y,
+    selection,
+    signal
+  }) {
+    const {
+      height,
+      width
+    } = this._getTileExtent(x, y);
+
+    const x0 = x * this.tileSize;
+    const y0 = y * this.tileSize;
+    const window = [x0, y0, x0 + width, y0 + height];
+    const image = await this._indexer(selection);
+    return this._readRasters(image, {
+      window,
+      width,
+      height,
+      signal
+    });
+  }
+
+  async _readRasters(image, props) {
+    var _props$signal;
+
+    const interleave = (0, _tiffUtils.isInterleaved)(this.shape);
+    const raster = await image.readRasters({
+      interleave,
+      ...props
+    });
+
+    if (props !== null && props !== void 0 && (_props$signal = props.signal) !== null && _props$signal !== void 0 && _props$signal.aborted) {
+      throw _tiffUtils.SIGNAL_ABORTED;
+    }
+
+    const data = interleave ? raster : raster[0];
+    return {
+      data,
+      width: raster.width,
+      height: raster.height
+    };
+  }
+
+  _getTileExtent(x, y) {
+    const {
+      height: zoomLevelHeight,
+      width: zoomLevelWidth
+    } = (0, _tiffUtils.getImageSize)(this);
+    let height = this.tileSize;
+    let width = this.tileSize;
+    const maxXTileCoord = Math.floor(zoomLevelWidth / this.tileSize);
+    const maxYTileCoord = Math.floor(zoomLevelHeight / this.tileSize);
+
+    if (x === maxXTileCoord) {
+      width = zoomLevelWidth % this.tileSize;
     }
-  }, {
-    key: "onTileError",
-    value: function onTileError(err) {
-      console.error(err);
+
+    if (y === maxYTileCoord) {
+      height = zoomLevelHeight % this.tileSize;
     }
-  }]);
-  return TiffPixelSource;
-}();
+
+    return {
+      height,
+      width
+    };
+  }
+
+  onTileError(err) {
+    console.error(err);
+  }
+
+}
 
 var _default = TiffPixelSource;
 exports.default = _default;